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Software Contributions


PopGenome

PopGenome is an efficient Swiss army knife for population genetics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is an R library optimized for speed (via the seamless integration of C code).
The software is available from the PopGenome homepage.

sybil

The R-package sybil is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks, such as flux-balance analysis (FBA) that is a mathematical technique to find fluxes in metabolic models at steady state.

Through fine-tuned communication with the optimization software, sybil is extremely fast when performing large sets of similar analyses. 
The software is available on CRAN. More information is available on the sybil homepage.

sybilSBML

Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read, write, and check 'SBML' files in 'sybil' provided.

sybilcycleFreeFlux

Implementing cycle-Free flux balance analysis allows to efficiently remove thermodynamically infeasible loops from flux distributions.
sybilcycleFreeFlux is available on CRAN.

sybilccFBA

This extension implements different techniques of cost constrained flux balance analysis:
1. MetabOlic Modeling with ENzyme kineTics 'MOMENT' which uses enzyme kinetic data and enzyme molecular weights to constrain flux balance analysis(FBA).
2. An improvement of 'MOMENT' that considers multi-functional enzymes 'ccFBA'.
sybilDynFBA is available on CRAN.

sybilDynFBA

The package sybilDynFBA is an extension to sybil in order to perform dynamic FBA.
sybilDynFBA is available on CRAN.

sybilFCF

The R-package sybilFCF computes extreme pathways and coupled reaction sets.

TreeSnatcher Plus

TreeSnatcher Plus is a GUI-driven Java application that recognizes bifurcating and multifurcating trees in pixel images (like JPG) and outputs the tree in Newick format.
The software is available at the TreeSnatcher Plus homepage

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